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BioC 3.2: CHECK report for ballgown on zin1

This page was generated on 2016-04-23 10:13:59 -0700 (Sat, 23 Apr 2016).

Package 71/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ballgown 2.2.0
Alyssa Frazee
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/ballgown
Last Changed Rev: 109589 / Revision: 116712
Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: ballgown
Version: 2.2.0
Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings ballgown_2.2.0.tar.gz
StartedAt: 2016-04-22 22:18:03 -0700 (Fri, 22 Apr 2016)
EndedAt: 2016-04-22 22:21:45 -0700 (Fri, 22 Apr 2016)
EllapsedTime: 222.6 seconds
RetCode: 0
Status:  OK 
CheckDir: ballgown.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings ballgown_2.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/ballgown.Rcheck’
* using R version 3.2.4 Revised (2016-03-16 r70336)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ballgown/DESCRIPTION’ ... OK
* this is package ‘ballgown’ version ‘2.2.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘ballgown’ can be installed ... [16s/16s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
subset,ballgown : .local: no visible binding for global variable ‘i_id’
subset,ballgown : .local: no visible binding for global variable ‘e_id’
subset,ballgown : .local: no visible binding for global variable ‘t_id’
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [24s/24s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.R’ [30s/30s]
 [30s/30s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.2-bioc/meat/ballgown.Rcheck/00check.log’
for details.


ballgown.Rcheck/00install.out:

* installing *source* package ‘ballgown’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a new generic function for ‘structure’ in package ‘ballgown’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (ballgown)

ballgown.Rcheck/ballgown-Ex.timings:

nameusersystemelapsed
annotate_assembly3.3980.0283.434
ballgown-class0.0790.0000.081
ballgown-constructor0.2280.0040.233
ballgownrsem3.1800.0043.181
bg0.0310.0000.031
checkAssembledTx000
clusterTranscripts0.1300.0000.131
collapseTranscripts0.2070.0000.206
contains2.0760.0082.083
dirs0.0310.0000.031
eexpr0.0340.0000.034
expr-replace0.0360.0000.036
expr0.0310.0000.030
exprfilter0.0560.0080.065
geneIDs0.0320.0000.031
geneNames0.8000.0040.803
getAttributeField1.2090.0001.209
getGenes0.7470.0000.768
gexpr0.0860.0000.085
gffRead0.2450.0000.245
gffReadGR0.7390.0040.744
iexpr0.0330.0000.033
indexes-replace0.0310.0000.030
indexes0.0320.0000.032
last0.0000.0000.001
mergedDate0.0310.0000.030
pData-replace0.0320.0000.032
pData0.0380.0000.038
pctOverlap1.1710.0001.170
plotLatentTranscripts0.0000.0000.001
plotMeans0.0000.0000.001
plotTranscripts0.0010.0000.000
sampleNames0.0340.0000.034
seqnames0.0350.0000.034
stattest0.0820.0040.086
structure0.0570.0000.057
subset0.1110.0040.115
tGene0.0400.0000.049
texpr0.0330.0000.036
transcriptIDs0.0310.0080.035
transcriptNames0.0330.0000.036
writeFiles0.0010.0000.000